Conservation managers need to be able to assess and prioritize issues that may affect their target habitats and species. In the Baie de Somme, France, conservation issues affecting overwintering shorebirds include hunting pressure, cockle fishing, recreational disturbance, Spartina encroachment, and changing sediment levels. We used an individual-based model to predict the effect of these issues on the survival of three shorebird species: dunlin Calidris alpina, oystercatcher Haematopus ostralegus and curlew Numenius arquata. In the model, removing hunting from the mudflats in the eastern part of the estuary had the greatest positive effect on shorebird survival. Oystercatcher survival decreased markedly when stocks of large cockles were reduced to <250 m-2 or numbers of fishermen per day were doubled. Short-term disturbance events, such as walkers, had more effect on shorebird survival than long-term events, such as fishermen. Dunlin, as a protected species, were able to feed outside the Réserve Naturelle and were unaffected by disturbance within the Réserve. Oystercatcher survival decreased when the number of disturbance events within the Réserve exceeded one h-1, and curlew survival when disturbance events exceeded six h-1. Spartina encroachment caused dunlin survival to decline steadily as feeding habitat was lost. Dunlin were also the species most affected by changes in sediment levels, likely to occur through either sedimentation or sea level rise.